wnt5b wingless-type MMTV integration site family, member 5b [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: wnt5bprovided by ZNC
Official Full Name: wingless-type MMTV integration site family, member 5bprovided by ZNC
Primary source: ZFIN:ZDB-GENE-980526-87
See related: Ensembl:ENSDARG00000102464 AllianceGenome:ZFIN:ZDB-GENE-980526-87
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: ppt; wnt5; wnt-5; wnt[b]; pipetail; CHUNP6928; id:ibd5111; wu:fk85g06
Summary: Enables signaling receptor binding activity. Involved in muscle cell differentiation; positive regulation of convergent extension involved in gastrulation; and positive regulation of non-canonical Wnt signaling pathway. Acts upstream of or within with a positive effect on midbrain-hindbrain boundary morphogenesis. Acts upstream of or within several processes, including convergent extension; skeletal system development; and vasculature development. Predicted to be located in extracellular region and membrane. Predicted to be active in extracellular space. Is expressed in several structures, including central nervous system; cranial cartilage; fin; germ ring; and mesoderm. Orthologous to human WNT5B (Wnt family member 5B). [provided by Alliance of Genome Resources, Oct 2024]
Orthologs: all
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Genomic context

Location:: chromosome: 4

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	4	NC_007115.7 (8532174..8665469)
105	previous assembly	GRCz10 (GCF_000002035.5)	4	NC_007115.6 (8531283..8662201)

Chromosome 4 - NC_007115.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Glypican 4 mediates Wnt transport between germ layers via signaling filopodia.
Title: Glypican 4 mediates Wnt transport between germ layers via signaling filopodia.
the chaperon Wls and its ligands Wnt9a and Wnt5b are expressed in the ectoderm, whereas juxtaposed chondrocytes express Frzb and Gpc4.
Title: Roles of Wnt pathway genes wls, wnt9a, wnt5b, frzb and gpc4 in regulating convergent-extension during zebrafish palate morphogenesis.
disruption of wls resulted in a significant loss of craniofacial bone, whereas lack of gpc4, wnt5b and wnt9a resulted in severely delayed endochondral ossification.
Title: Distinct requirements of wls, wnt9a, wnt5b and gpc4 in regulating chondrocyte maturation and timing of endochondral ossification.
novel mechanism for Wnt5b and Gpc4 regulation of chondrocyte behavior that is independent of the core Wnt/PCP molecules and differs from their collaborative action of controlling cell movements during gastrulation
Title: A role of glypican4 and wnt5b in chondrocyte stacking underlying craniofacial cartilage morphogenesis.
In embryos overexpressing lbx1b, wnt5b, a ligand of the non-canonical Wnt/planar cell polarity (PCP) pathway, was significantly downregulated.
Title: Functional Investigation of a Non-coding Variant Associated with Adolescent Idiopathic Scoliosis in Zebrafish: Elevated Expression of the Ladybird Homeobox Gene Causes Body Axis Deformation.
Swap70b and Def6a delineate Wnt11 and Wnt5b signalling pathways and have roles in convergent and extension cell movement during zebrafish gastrulation
Title: Swap70b is required for convergent and extension cell movement during zebrafish gastrulation linking Wnt11 signalling and RhoA effector function.
CNBP up-regulates tbx2b and smarca5, and down-regulates wnt5b gene expression.
Title: Beyond the binding site: in vivo identification of tbx2, smarca5 and wnt5b as molecular targets of CNBP during embryonic development.
def6 morphants phenocopy Wnt5b mutants and ectopic overexpression of def6 essentially rescues Wnt5b morphants, indicating a novel role for def6 as a central GEF downstream of Wnt5b signaling
Title: Def6 is required for convergent extension movements during zebrafish gastrulation downstream of Wnt5b signaling.
identify rgs3 as having an overlapping expression pattern with wnt5b in zebrafish and reveal that individual knockdown of either rgs3 or wnt5b gene function produces similar somite patterning defects.
Title: Regulator of g protein signaling 3 modulates wnt5b calcium dynamics and somite patterning.
Data suggest that full-length Ryk conveys Wnt5b signals in a directional manner during gastrulation.
Title: Wnt5b-Ryk pathway provides directional signals to regulate gastrulation movement.

Submit: New GeneRIF Correction See all GeneRIFs (13)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WNT5 (e-PCR)
- UniSTS:205320

fd10f12.y1 (e-PCR)
- UniSTS:195120

fc44g06.x1 (e-PCR)
- UniSTS:203924

wnt5a (e-PCR), detects polymorphism
- UniSTS:205467

fk85g06.x1 (e-PCR)
- UniSTS:201634

fj03g10.x1 (e-PCR)
- UniSTS:198329

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables cytokine activity	IBA Inferred from Biological aspect of Ancestor more info
enables frizzled binding	IBA Inferred from Biological aspect of Ancestor more info
enables signaling receptor binding	IEA Inferred from Electronic Annotation more info
enables signaling receptor binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within Wnt signaling pathway, calcium modulating pathway	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within Wnt signaling pathway, calcium modulating pathway	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within ameboidal-type cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within angiogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in animal organ development	IEA Inferred from Electronic Annotation more info
involved_in canonical Wnt signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cartilage morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cell fate commitment	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cell migration involved in gastrulation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within cell migration involved in gastrulation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within chondrocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within convergent extension	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within convergent extension involved in axis elongation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within convergent extension involved in axis elongation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within convergent extension involved in gastrulation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within convergent extension involved in gastrulation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within dorsal convergence	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic body morphogenesis	IMP Inferred from Mutant Phenotype more info
acts_upstream_of_or_within embryonic cranial skeleton morphogenesis	IMP Inferred from Mutant Phenotype more info
acts_upstream_of_or_within embryonic viscerocranium morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within endochondral ossification	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within endocrine pancreas development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within fin regeneration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within intracellular sphingolipid homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within lymphangiogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within_positive_effect midbrain-hindbrain boundary morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within_positive_effect midbrain-hindbrain boundary morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in muscle cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuromast development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within ossification	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within otolith development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of convergent extension involved in gastrulation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of non-canonical Wnt signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of serine C-palmitoyltransferase activity	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within post-anal tail morphogenesis	IMP Inferred from Mutant Phenotype more info
acts_upstream_of_or_within regulation of Wnt signaling pathway, calcium modulating pathway	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within regulation of Wnt signaling pathway, calcium modulating pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within release of sequestered calcium ion into cytosol	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within skeletal system development	IMP Inferred from Mutant Phenotype more info
acts_upstream_of_or_within somite development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within thrombocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within unidimensional cell growth	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in extracellular region	IEA Inferred from Electronic Annotation more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: protein Wnt-5b

Names: pipe tail

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001362273.1 → NP_001349202.1 protein Wnt-5b precursor

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same protein.

Source sequence(s)

BX649324, BX842699

UniProtKB/Swiss-Prot

A5WVR7, Q92050

UniProtKB/TrEMBL

B3DI33

Conserved Domains (1) summary

pfam00110
Location:54 → 363

wnt; wnt family
NM_130937.2 → NP_571012.1 protein Wnt-5b precursor

See identical proteins and their annotated locations for NP_571012.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 both encode the same protein.

Source sequence(s)

BX649324, BX842699

UniProtKB/Swiss-Prot

A5WVR7, Q92050

UniProtKB/TrEMBL

B3DI33

Related

ENSDARP00000134193.1, ENSDART00000162065.2

Conserved Domains (1) summary

pfam00110
Location:54 → 363

wnt; wnt family